A method of making a noninvasive molecular control and analysis is described. The method of making the noninvasive molecular control includes, predetermining a positive control for a condition of interest, selecting a cell line with a control marker for the condition of interest, amplifying release of cfDNA from the selected cell line, isolating the released cfDNA from the selected cell line, quantifying the control marker from the isolated cfDNA, determining a volume of the control marker for addition to an isolated control plasma, isolating the control plasma from a control sample, treating the isolated control plasma with a control stabilizer, determining a volume of the control plasma to add to the volume of control marker, combining the volume of the control marker with the isolated control plasma, and analyzing a sample against the noninvasive molecular control to determine the presence or absence of a condition of interest.